The interpretation and application of results of quantitative trait locus (QTL) studies to crop improvement are usually limited by lack of information on metabolic pathways responsible for agronomic traits. An exception is antibotic resistance to the corn earworm (CEW) by the C-glycosyl flavone, maysin, synthesized in maize silks via a branch of the well-characterized flavonoid pathway. Since cDNA probes are available for both structural and regulatory loci for the pathway we have used this system as a model to define the nature of genes for QTL for maysin synthesis. The two most intriguing results from this study were: 1) The importance of regulatory as opposed to structural loci in determining maysin content and CEW resistance and 2) The regulatory loci identified were not only controlling the structural genes required for maysin, but also the regulatory loci of the interconnecting anthocyanin pathway.